In nucleic acid sequencing, mutation detection, proteomics, and gene expression analysis, there is a growing emphasis on the use of high density arrays of immobilized nucleic acid or polypeptide probes. Such arrays can be prepared by a variety of approaches, e.g., by depositing biopolymers, for example, cDNAs, oligonucleotides or polypeptides on a suitable surface, or by using photolithographic techniques to synthesize biopolymers directly on a suitable surface. Arrays constructed in this manner are typically formed in a planar area of between about 4–100 mm2, and can have densities of up to several thousand or more distinct array members per cm2.
In use, an array surface is contacted with a labeled sample containing target analytes (usually nucleic acids or proteins) under conditions that promote specific, high-affinity binding of the analytes in the sample to one or more of the probes present on the array. The goal of this procedure is to quantify the level of binding of one or more probes of the array to labeled analytes in the sample. Typically, the analytes in the sample are labeled with a detectable label such as a fluorescent tag, and quantification of the level of fluorescence associated with a bound probe represents a direct measurement of the level of binding. In turn, this measurement of binding represents an estimate of the abundance of a particular analyte in the sample. A variety of biological and/or chemical compounds may be used as detectable labels in the above-described arrays (See, e.g., Wetmur, J. Crit Rev Biochem and Mol Bio 26:227, 1991; Mansfield et al., Mol Cell Probes. 9:145–56, 1995; Kricka, Ann Clin Biochem. 39:114–29, 2002).
Such arrays are commonly used to perform nucleic acid hybridization assays. Generally, in such a hybridization assay, labeled single-stranded analyte nucleic acid (e.g. polynucleotide target) is hybridized to an immobilized complementary single-stranded nucleic acid probe. Complementary nucleic acid probe binds the labeled target polynucleotide, and the presence of the labeled target polynucleotide of interest is detected and quantified.
Such arrays often contain sectors that may be independently contacted with a sample. These sectors, by virtue of design or by as a consequence of the method by which an array is made, are usually spatially separated from each other, and may be each separately contacted with a different sample in a single hybridization experiment. Such multi-sector arrays are of great use in diagnostic and drug screening applications where one or more samples are incubated with multiple sets of probes, where each set of probes is contained in isolated sectors on the same substrate.
A drawback of strategies that involve contacting more than one sample with a multi-sector array is that cross-contamination may occur between the samples during the time that they are in contact with the array. Sample cross-contamination causes probes contained in one sector of an array to bind targets in the cross-contaminated sample. As a consequence, the data obtained from that sector may be of inferior quality and may not be reliable.
As such, methods of detecting cross-contamination between samples contacted with different sectors of a multi-sector array are needed.
Conventional methods for detecting cross-contamination involve testing of results by binary swapping (i.e., two-way testing) the targets, probes and dye labeling. Such methods, although they are quite effective, are tedious and costly in terms of the number of microarrays used to perform the methods, and the time spent performing the methods and analyzing the results.
As such, there is a need for inexpensive methods of detecting cross-contamination between samples contacted with different sectors of a multi-sector array. This invention meets this, and other, needs.